6V92

RSC-NCP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 20.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement.

Patel, A.B.Moore, C.M.Greber, B.J.Luo, J.Zukin, S.A.Ranish, J.Nogales, E.

(2019) Elife 8

  • DOI: https://doi.org/10.7554/eLife.54449
  • Primary Citation of Related Structures:  
    6V8O, 6V92

  • PubMed Abstract: 

    Eukaryotic DNA is packaged into nucleosome arrays, which are repositioned by chromatin remodeling complexes to control DNA accessibility. The Saccharomyces cerevisiae RSC ( R emodeling the S tructure of C hromatin) complex, a member of the SWI/SNF chromatin remodeler family, plays critical roles in genome maintenance, transcription, and DNA repair. Here, we report cryo-electron microscopy (cryo-EM) and crosslinking mass spectrometry (CLMS) studies of yeast RSC complex and show that RSC is composed of a rigid tripartite core and two flexible lobes. The core structure is scaffolded by an asymmetric Rsc8 dimer and built with the evolutionarily conserved subunits Sfh1, Rsc6, Rsc9 and Sth1. The flexible ATPase lobe, composed of helicase subunit Sth1, Arp7, Arp9 and Rtt102, is anchored to this core by the N-terminus of Sth1. Our cryo-EM analysis of RSC bound to a nucleosome core particle shows that in addition to the expected nucleosome-Sth1 interactions, RSC engages histones and nucleosomal DNA through one arm of the core structure, composed of the Rsc8 SWIRM domains, Sfh1 and Npl6. Our findings provide structural insights into the conserved assembly process for all members of the SWI/SNF family of remodelers, and illustrate how RSC selects, engages, and remodels nucleosomes.


  • Organizational Affiliation

    Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 7477Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear protein STH1/NPS1B [auth R]1,359Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.4.12
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-like protein ARP9C [auth B]467Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Regulator of Ty1 transposition protein 102D [auth P]157Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
High temperature lethal protein 1E [auth C]78Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex protein RSC14F [auth D]180Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex subunit RSC7G [auth E]435Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex subunit RSC2H [auth F]889Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex protein RSC3I [auth G]885Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex subunit RSC4J [auth H]625Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex protein RSC8K [auth I],
L [auth J],
M [auth K],
N [auth L]
557Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex protein RSC6O [auth M]483Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex subunit RSC9P [auth N]581Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex protein RSC58Q [auth O]502Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex subunit SFH1R [auth Q]426Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin structure-remodeling complex protein RSC30883Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown ProteinT [auth 2]28Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown ProteinU [auth 3],
V [auth 4]
19Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown ProteinW [auth 5]14Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Uuknown ProteinX [auth 6]15Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown ProteinY [auth 7]49Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1BA [auth a],
FA [auth e]
136Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4CA [auth b],
GA [auth f]
103Homo sapiensMutation(s): 0 
Gene Names: 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/EDA [auth c],
HA [auth g]
130Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFA
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PHAROS:  P04908
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-KEA [auth d],
IA [auth h]
126Homo sapiensMutation(s): 0 
Gene Names: H2BC12H2BFTHIRIP1HIST1H2BK
UniProt & NIH Common Fund Data Resources
Find proteins for O60814 (Homo sapiens)
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PHAROS:  O60814
GTEx:  ENSG00000197903 
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Entity ID: 22
MoleculeChains LengthOrganismImage
DNA (146-MER)AA [auth j],
Z [auth i]
146synthetic construct
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
JA [auth I]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 20.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM63072
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35-GM127018

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references